[ { "id": "est_sfs", "name": "est sfs", "article": "https:\/\/doi.org\/10.1534\/genetics.118.301120", "website": "https:\/\/sourceforge.net\/projects\/est-usfs\/", "git": "", "description": "BLAST programs search nucleotide databases using a nucleotide query", "version": "2.04", "documentation": "https:\/\/sourceforge.net\/projects\/est-usfs\/", "multiqc": "custom", "commands": [ { "name": "est_sfs", "cname": "est_sfs", "command": "est-sfs", "category": "other", "output_dir": "est_sfs", "inputs": [ { "name": "sfs_vcf", "type": "sfs", "description": "(Required) sfs count file generate from vcf" }, { "name": "sfs_outgroup1", "type": "sfs", "description": "(Required) sfs count file from outgroup1" }, { "name": "sfs_outgroup2", "type": "sfs", "description": "(Optional) sfs count file from outgroup2" }, { "name": "sfs_outgroup3", "type": "sfs", "description": "(Optional) sfs count file from outgroup3" } ], "outputs": [ { "name": "aatsv", "type": "tsv", "file": "output-file-AA.tsv", "description": "TSV file with CHR POS0 AA (Ancestral Allele) informations" }, { "name": "est_sfs_output_aa", "type": "tsv", "file": "est-sfs-output-withAA.tsv", "description": "est sfs output with est-sfs input information, pvalue information and ancestral allele information." } ], "options": [ { "name": "est_sfs_threads", "prefix": "--threads", "type": "numeric", "value": 8, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "est_sfs_method_order_outgroup", "prefix": "", "type": "select", "choices": [ { "Mean_percent_identity": 2 }, { "Number_Nucleotide_Homology_inOutgroup": 3 } ], "value": 2, "label": "Method to order outgroups compared with focal species." }, { "name": "est_sfs_model", "type": "select", "choices": [ { "Jukes-Cantor-model": "0" }, { "Kimura-2-parameter-model": "1" }, { "Rate-6-model": "2" } ], "value": "1", "label": "Nucleotide substitution model in est-sfs." }, { "name": "est_sfs_nrandom", "prefix": "", "type": "numeric", "value": 3, "min": 0, "max": 100, "step": 1, "label": "The algorithm returns the highest log likelihood found in nrandom runs" }, { "name": "est_sfs_seed", "prefix": "", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "Positive integer used as seed. If set to 0, a random seed is used and writen to log file." }, { "name": "est_sfs_threshold", "prefix": "", "type": "numeric", "value": 0.95, "min": 0.5, "max": 1, "step": 0.01, "label": "Probality threshold for variant orientation support by est-sfs." }, { "name": "est_sfs_min_outgroup", "prefix": "", "type": "numeric", "value": 1, "min": 0, "max": 3, "step": 1, "label": "Minimum number of outgroup with a nucletide homology required to accept ancestral allele support by est-sfs." }, { "name": "est_sfs_ldhelmet", "prefix": "", "type": "checkbox", "value": false, "label": "Convert est-sfs probilities into LDhelmet input format (Ancestral allele priors)" } ] } ], "prepare_report_script": "est_sfs.prepare.report.py", "prepare_report_outputs": [ "estimated_uSFS_plot_mqc.png" ], "install": [], "citations": { "est-sfs": [ "Keightley, P. D and Jackson B. C. (2018). Inferring the probability of the derived versus the ancestral allelic state at a polymorphic site. Genetics 209: 897-906." ], "parallel": [ "Tange, O. (2023, May 22). GNU Parallel 20230522 ('Charles'). Zenodo. https:\/\/doi.org\/10.5281\/zenodo.7958356." ] }, "yaml": "{\n id: est_sfs,\n name: est sfs,\n article: https:\/\/doi.org\/10.1534\/genetics.118.301120,\n website: \"https:\/\/sourceforge.net\/projects\/est-usfs\/\",\n git: \"\",\n description: \"BLAST programs search nucleotide databases using a nucleotide query\",\n version: \"2.04\",\n documentation: \"https:\/\/sourceforge.net\/projects\/est-usfs\/\",\n multiqc: \"custom\", # from mbb_mqc_plugin\n commands:\n [\n {\n name: \"est_sfs\",\n cname: \"est_sfs\",\n command: \"est-sfs\",\n category: \"other\",\n output_dir: \"est_sfs\",\n inputs: \n [\n { name: sfs_vcf, type: \"sfs\", description: \"(Required) sfs count file generate from vcf\" }, \n { name: sfs_outgroup1, type: \"sfs\", description: \"(Required) sfs count file from outgroup1\" },\n { name: sfs_outgroup2, type: \"sfs\", description: \"(Optional) sfs count file from outgroup2\" },\n { name: sfs_outgroup3, type: \"sfs\", description: \"(Optional) sfs count file from outgroup3\" }\n ],\n outputs:\n [\n { name: aatsv, type: \"tsv\", file: \"output-file-AA.tsv\", description: \"TSV file with CHR POS0 AA (Ancestral Allele) informations\" },\n { name: est_sfs_output_aa, type: \"tsv\", file: \"est-sfs-output-withAA.tsv\", description: \"est sfs output with est-sfs input information, pvalue information and ancestral allele information.\" }\n ],\n options:\n [\n {\n name: est_sfs_threads,\n prefix: \"--threads\",\n type: numeric,\n value: 8,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: \"est_sfs_method_order_outgroup\",\n prefix: \"\",\n type: select,\n choices: [\n Mean_percent_identity: 2,\n Number_Nucleotide_Homology_inOutgroup: 3,\n ],\n value: 2,\n label: \"Method to order outgroups compared with focal species.\",\n },\n {\n name: est_sfs_model,\n type: select,\n choices: [\n Jukes-Cantor-model: \"0\",\n Kimura-2-parameter-model: \"1\",\n Rate-6-model: \"2\",\n ],\n value: \"1\",\n label: \"Nucleotide substitution model in est-sfs.\"\n },\n {\n name: \"est_sfs_nrandom\",\n prefix: \"\",\n type: numeric,\n value: 3,\n min: 0,\n max: 100,\n step: 1,\n label: \"The algorithm returns the highest log likelihood found in nrandom runs\",\n },\n {\n name: \"est_sfs_seed\",\n prefix: \"\",\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"Positive integer used as seed. If set to 0, a random seed is used and writen to log file.\",\n },\n {\n name: \"est_sfs_threshold\",\n prefix: \"\",\n type: numeric,\n value: 0.95,\n min: 0.5,\n max: 1,\n step: 0.01,\n label: \"Probality threshold for variant orientation support by est-sfs.\",\n },\n {\n name: \"est_sfs_min_outgroup\",\n prefix: \"\",\n type: numeric,\n value: 1,\n min: 0,\n max: 3,\n step: 1,\n label: \"Minimum number of outgroup with a nucletide homology required to accept ancestral allele support by est-sfs.\",\n },\n {\n name: \"est_sfs_ldhelmet\",\n prefix: \"\",\n type: checkbox,\n value: False,\n label: \"Convert est-sfs probilities into LDhelmet input format (Ancestral allele priors)\",\n },\n ],\n },\n ],\n prepare_report_script: est_sfs.prepare.report.py,\n prepare_report_outputs: [\n estimated_uSFS_plot_mqc.png,\n ],\n install: {\n # gsl: [\n # \"cd \/opt\/biotools\/\",\n # \"wget https:\/\/ftp.gnu.org\/gnu\/gsl\/gsl-latest.tar.gz\",\n # \"tar -xf gsl-latest.tar.gz\",\n # \"cd gsl-2.7.1\/\",\n # \".\/configure && make && make install\",\n # \"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\/usr\/local\/lib\",\n # \"export PATH=$PATH:\/opt\/biotools\/gsl-2.7.1\/\",\n # ],\n # est-sfs: [\n # \"cd \/opt\/biotools\/\",\n # \"wget https:\/\/kumisystems.dl.sourceforge.net\/project\/est-usfs\/est-sfs-release-2.04.tar.gz\",\n # \"tar -xf est-sfs-release-2.04.tar.gz\",\n # \"cd est-sfs-release-2.04\",\n # \"make\"\n # \"export PATH=$PATH:\/opt\/biotools\/est-sfs-release-2.04\/\",\n # ],\n },\n citations: {\n est-sfs: [\n \"Keightley, P. D and Jackson B. C. (2018). Inferring the probability of the derived versus the ancestral allelic\nstate at a polymorphic site. Genetics 209: 897-906.\"\n ],\n parallel: [\n \"Tange, O. (2023, May 22). GNU Parallel 20230522 ('Charles'). Zenodo. https:\/\/doi.org\/10.5281\/zenodo.7958356.\"\n ]\n }\n}\n" } ]