galaxscript_profiles: Builds all input files and an script to run all analyses from...

In diegosasso/ontobayes: Ontology-aware Bayesian Phylogenetic Information Analysis of Morphological Data

Builds all input files and an script to run all analyses from ontobayes_profiles in Galax.

Description

Builds all input files and an script to run all analyses from ontobayes_profiles in Galax.

Usage

galaxscript_profiles(
  tags = tags,
  runs = 2,
  burnin = 251,
  OS = "windows",
  filename = "galaxscript"
)

Arguments

tags	list, profiles with anatomy ontology terms to query. The list of profiles should be organized as indicated in the examples.
runs	integer, the number of independent runs of mcmc used in the MrBayes commands block. Default is set to 2.
burnin	integer, the absolute number of trees as the burn-in used in the mcmc. Default is set to 251.
OS	character, sets the operational system to produce batch files for. Options are "windows" and "unix". Default is set to "windows".
filename	character, name of the output file.

Value

All necessary input files, organized in subfolders inside the GALAX/INPUT folder, and an script to run all Galax analyses.

Examples

## Not run: 
# HAO example #
# List of profiles with terms to query #
tags <- list(
  c("HAO:0000506", "HAO:0000513", "HAO:0000453"),
  c("HAO:0000234", "HAO:0001003"),
  c("HAO:0000874", "HAO:0000583", "HAO:0000630"))

# Set profile names and terms #
names(tags) <- c("mouthparts_profile1", "head_profile2", "mesosoma_profile3")
names(tags[[1]]) <- c("mandible", "maxilla", "labium")
names(tags[[2]]) <- c("cranium", "tentorium")
names(tags[[3]]) <- c("prothorax", "mesothorax", "metathorax")

# Creates bat file to run all analyses on Galax #
galaxscript_profiles(tags = tags, runs = 2, burnin = 251, OS = "windows", filename = "galaxprof1")

# UBERON example #
# List of profiles with terms to query #
tags <- list(
  c("UBERON_0002244", "UBERON_0002397", "UBERON_0004742"),
  c("UBERON_2000658", "UBERON_2000488"),
  c("UBERON_0000151", "UBERON_0000152", "UBERON_0003097"))

# Set profile names and terms #
names(tags) <- c("jaw_profile1", "pharynx_profile2", "fins_profile3")
names(tags[[1]]) <- c("premaxilla", "maxilla", "dentary")
names(tags[[2]]) <- c("epibranchial_bone", "ceratobranchial_bone")
names(tags[[3]]) <- c("pectoral_fin", "pelvic_fin", "dorsal_fin")

# Creates bat file to run all analyses on Galax #
galaxscript_profiles(tags = tags, runs = 2, burnin = 251, OS = "windows", filename = "galaxprof2")

## End(Not run)

diegosasso/ontobayes documentation built on May 3, 2022, 10:23 p.m.