[ { "id": "moments2Dinfer", "name": "moments infer 2D model", "article": "10.1534\/genetics.117.200493", "website": "https:\/\/bitbucket.org\/simongravel\/moments\/", "git": "https:\/\/bitbucket.org\/simongravel\/moments\/src\/master\/", "description": "moments implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum.", "version": "1.1.16", "documentation": "https:\/\/moments.readthedocs.io\/", "multiqc": "custom", "commands": [ { "name": "moments2Dinfer", "command": "", "category": "genet_pop", "output_dir": "moments2Dinfer", "inputs": [ { "name": "vcfFile", "type": "vcf_file", "description": "A vcf file to compute a SFS from" }, { "name": "popmap_file", "type": "popmap", "file": "", "description": "Path to tsv file with samples group" } ], "outputs": [ { "name": "moments2DinferDone", "type": "txt", "file": "moments2DinferDone.txt", "description": "Demographic inference is done" } ], "options": [ { "name": "moments2Dinfer_polarized", "prefix": null, "type": "checkbox", "value": false, "label": "If True, the data are assumed to be correctly polarized by 'outgroup_allele'" }, { "name": "moments2Dinfer_projections", "prefix": "--projections", "type": "numeric", "value": 20, "min": 10, "max": 1000, "step": 1, "label": "sample sizes to project down to for each population." }, { "name": "moments2Dinfer_model", "prefix": "", "type": "select", "choices": [ { "Strict Isolation.": "SI" }, { "Strict Isolation with exponential size changes.": "SIexp" }, { "Strict Isolation with heterogeneous Ne (shared between populations).": "SI2N" }, { "Isolation with Migration.": "IM" }, { "Isolation with Migration with exponential size changes.": "IMexp" }, { "Isolation with Migration with heterogeneous Ne (shared between populations).": "IM2N" }, { "Isolation with Migration with heterogeneous Me (shared between populations).": "IM2M" }, { "Isolation with Migration with heterogeneous Me (population-specific).": "IM2M2P" }, { "Isolation with Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).": "IM2N2M" }, { "Isolation with Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).": "IM2N2M2P" }, { "Secondary Contact.": "SC" }, { "Secondary Contact with exponential size changes.": "SCexp" }, { "Secondary Contact with heterogeneous Ne (shared between populations).": "SC2N" }, { "Secondary Contact with heterogeneous Me (shared between populations).": "SC2M" }, { "Secondary Contact with heterogeneous Me (population-specific).": "SC2M2P" }, { "Secondary Contact with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).": "SC2N2M" }, { "Secondary Contact with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).": "SC2N2M2P" }, { "Ancient Migration.": "AM" }, { "Ancient Migration with exponential size changes.": "AMexp" }, { "Ancient Migration with heterogeneous Ne (shared between populations).": "AM2N" }, { "Ancient Migration with heterogeneous Me (shared between populations).": "AM2M" }, { "Ancient Migration with heterogeneous Me (population-specific).": "AM2M2P" }, { "Ancient Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).": "AM2N2M" }, { "Ancient Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).": "AM2N2M2P" } ], "value": "SI", "label": "Migration Model" }, { "name": "moments2Dinfer_optimizer", "prefix": "", "type": "select", "choices": [ { "BFGS algorithm": "optimize_log" }, { "L-BFGS-B algorithm": "optimize_log_lbfgsb" }, { "downhill simplex on log params": "optimize_log_fmin" }, { "Powell method on slices of parameter space sequentially": "optimize_log_powell" }, { "Modified version of scipy dual_anneal": "optimize_dual_anneal" } ], "value": "optimize_log", "label": "given a demographic model and a set of parameters, Optimzation method find those parameters that minimize the negative log-likelihood of the data given the model" }, { "name": "moments2Dinfer_MaxIter", "prefix": "", "type": "numeric", "value": 1, "min": 1, "max": 100, "step": 1, "label": "How long the optimizer will run" }, { "name": "moments2Dinfer_firstpop", "prefix": "", "type": "numeric", "value": 1, "min": 1, "max": 50, "step": 1, "label": "index of the first population to analyse" }, { "name": "moments2Dinfer_secondpop", "prefix": "", "type": "numeric", "value": 2, "min": 1, "max": 50, "step": 1, "label": "index of the second population to analyse" }, { "name": "moments2Dinfer_mutation", "prefix": "", "type": "numeric", "value": 2, "min": 1, "max": 50, "step": 1, "label": "mutation rate in %" }, { "name": "moments2Dinfer_gtime", "prefix": "", "type": "numeric", "value": 20, "min": 1, "max": 100, "step": 1, "label": "generation time in years" } ] } ], "assets": [ "models_and_params.txt", "moments_models_2pop.py", "local_Misc.py", "local_scipy_dual_anneal.py", "moments_inference_dualanneal.py" ], "install": [], "citations": { "moments": [ "Jouganous, J., Long, W., Ragsdale, A. P., & Gravel, S. (2017). Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics, 206(3), 1549-1567. doi: 10.1534\/genetics.117.200493" ] }, "yaml": "{\n id: moments2Dinfer,\n name: moments infer 2D model,\n article: \"10.1534\/genetics.117.200493\",\n website: \"https:\/\/bitbucket.org\/simongravel\/moments\/\",\n git: \"https:\/\/bitbucket.org\/simongravel\/moments\/src\/master\/\",\n description: \"moments implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum.\",\n version: \"1.1.16\",\n documentation: \"https:\/\/moments.readthedocs.io\/\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: moments2Dinfer,\n command: \"\",\n category: \"genet_pop\",\n output_dir: moments2Dinfer,\n inputs: [\n { name: vcfFile, type: \"vcf_file\", description: \"A vcf file to compute a SFS from\"},\n { name: popmap_file, type: \"popmap\", file: \"\", description: \"Path to tsv file with samples group\"}\n ],\n outputs: [{ name: moments2DinferDone, type: \"txt\",file: \"moments2DinferDone.txt\", description: \"Demographic inference is done\" }],\n options: [\n {\n name: moments2Dinfer_polarized,\n prefix: ,\n type: checkbox,\n value: FALSE,\n label: \"If True, the data are assumed to be correctly polarized by 'outgroup_allele'\",\n },\n {\n name: moments2Dinfer_projections,\n prefix: --projections,\n type: numeric,\n value: 20,\n min: 10,\n max: 1000,\n step: 1,\n label: \"sample sizes to project down to for each population.\",\n },\n {\n name: \"moments2Dinfer_model\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n Strict Isolation.: \"SI\",\n Strict Isolation with exponential size changes.: \"SIexp\",\n Strict Isolation with heterogeneous Ne (shared between populations).: \"SI2N\",\n Isolation with Migration.: \"IM\",\n Isolation with Migration with exponential size changes.: \"IMexp\",\n Isolation with Migration with heterogeneous Ne (shared between populations).: \"IM2N\",\n Isolation with Migration with heterogeneous Me (shared between populations).: \"IM2M\",\n Isolation with Migration with heterogeneous Me (population-specific).: \"IM2M2P\",\n Isolation with Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).: \"IM2N2M\",\n Isolation with Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).: \"IM2N2M2P\",\n Secondary Contact.: \"SC\",\n Secondary Contact with exponential size changes.: \"SCexp\",\n Secondary Contact with heterogeneous Ne (shared between populations).: \"SC2N\",\n Secondary Contact with heterogeneous Me (shared between populations).: \"SC2M\",\n Secondary Contact with heterogeneous Me (population-specific).: \"SC2M2P\",\n Secondary Contact with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).: \"SC2N2M\",\n Secondary Contact with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).: \"SC2N2M2P\",\n Ancient Migration.: \"AM\",\n Ancient Migration with exponential size changes.: \"AMexp\",\n Ancient Migration with heterogeneous Ne (shared between populations).: \"AM2N\",\n Ancient Migration with heterogeneous Me (shared between populations).: \"AM2M\",\n Ancient Migration with heterogeneous Me (population-specific).: \"AM2M2P\",\n Ancient Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (shared between populations).: \"AM2N2M\",\n Ancient Migration with heterogeneous Ne (shared between populations) and heterogeneous Me (population-specific).: \"AM2N2M2P\"\n ],\n value: \"SI\",\n label: \"Migration Model\",\n },\n {\n name: \"moments2Dinfer_optimizer\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n BFGS algorithm: \"optimize_log\",\n L-BFGS-B algorithm: \"optimize_log_lbfgsb\",\n downhill simplex on log params: \"optimize_log_fmin\",\n Powell method on slices of parameter space sequentially: \"optimize_log_powell\",\n Modified version of scipy dual_anneal: \"optimize_dual_anneal\",\n ],\n value: \"optimize_log\",\n label: \"given a demographic model and a set of parameters, Optimzation method find those parameters that minimize the negative log-likelihood of the data given the model\",\n },\n {\n name: \"moments2Dinfer_MaxIter\",\n prefix: \"\",\n type: numeric,\n value: 1,\n min: 1,\n max: 100,\n step: 1,\n label: \"How long the optimizer will run\"\n }, \n {\n name: moments2Dinfer_firstpop,\n prefix: \"\",\n type: numeric,\n value: 1,\n min: 1,\n max: 50,\n step: 1,\n label: \"index of the first population to analyse\",\n },\n {\n name: moments2Dinfer_secondpop,\n prefix: \"\",\n type: numeric,\n value: 2,\n min: 1,\n max: 50,\n step: 1,\n label: \"index of the second population to analyse\",\n },\n {\n name: moments2Dinfer_mutation,\n prefix: \"\",\n type: numeric,\n value: 2,\n min: 1,\n max: 50,\n step: 1,\n label: \"mutation rate in %\",\n },\n {\n name: moments2Dinfer_gtime,\n prefix: \"\",\n type: numeric,\n value: 20,\n min: 1,\n max: 100,\n step: 1,\n label: \"generation time in years\",\n },\n ],\n },\n ],\n assets: [\"models_and_params.txt\",\"moments_models_2pop.py\",\"local_Misc.py\",\"local_scipy_dual_anneal.py\",\"moments_inference_dualanneal.py\"], \n install:\n {\n # moments: [\n # 'pip3 install cython==0.29.0',\n # 'pip3 install git+https:\/\/bitbucket.org\/simongravel\/moments.git '\n # ],\n },\n citations:\n {\n moments: [\n \"Jouganous, J., Long, W., Ragsdale, A. P., & Gravel, S. (2017). Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics, 206(3), 1549-1567. doi: 10.1534\/genetics.117.200493\"\n ],\n },\n}\n" } ]