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Process an XML template with TOML config.

Source: R/process_template.r
process_template.Rd

process_template will parse TOML config with three different blocks, xml containing additional xml chunks that will be processed independently, templates containing file paths relative to the parsed TOML config) to additional TOML configs and defaults contain default parameters for main template, xml chunks contained in the TOML config or any subtemplates linked in the TOML config. The xml chunks and any parameters are then substituted to the template according to moustache tags.

Usage

process_template(
  template,
  output,
  config = NULL,
  alignment = NULL,
  format = NULL,
  parameters = NULL
)

Arguments

template

an XML template with moustache tags that will be substituted according to the input parameters or the default parameters in the TOML config.

output

processed template

config

a TOML config file containing default values for moustache tags, XML chunks or path to additional TOML subconfigs/subtemplates.

alignment

sequence alignment

format

of the sequence alignment

parameters

these will replace the parameters with the same name in the TOML config or any TOML subconfigs/subtemplates

Details

First the function will recursively parse any TOML configs linked in the template block and then process XML chunks by substituting the moustache tags using the content of the default block and any parameters from the parent TOML config. After that, processed XML chunks as well as any other values in default block of TOML config or from input parameters are substituted into the XML template according to the present moustache tags.

There are two different ways how parameters and xml chunks sharing the same name are merged. Parameters will overwrite parameters with the same name in their daughter config. This means that subtemplates/subconfigs can be shared by different TOML configs and be parametrized according to their need. On the other hand, xml chunks with the same name are merged together as a list, this makes it possible for different subtemplates to define their own priors, operators or logs, which can be then put in a single point without replacing each other's structures. This makes it possible to build a BEAST2 XML.

In addition, alignment in format FASTA or NEXUS can be specified and will be inputted as sequences tag. If not specified, the alignmet data type will be guessed and the alignment id will be constructed out of the alignment file.