MetaPhlAn

MetaPhlAn is a tool for profiling the composition of microbial communities. For more information, see the tool's website or Github wiki.

Function Call

toolchest.metaphlan(
    inputs,
    output_path=None,
    output_primary_name="out.txt",
    tool_args="",
    is_async=False,
)
toolchest$metaphlan(
    inputs,
    output_path = NULL,
    output_primary_name = "out.txt",
    tool_args = "",
    is_async = FALSE
)

Function Arguments

ArgumentUse in place of:Description
inputsinput file locationPath to one or more files to use as input. The files can be a local or remote, see Inputs and Outputs.
output_pathoutput file location(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Inputs and Outputs.
tool_argsall other arguments(optional) Additional arguments to be passed to MetaPhlAn. This should be a string of arguments like the command line.
output_primary_name(optional) Sets the name of the main output file. Defaults to "out.txt"
is_asyncWhether to run a job asynchronously. See Async Runs for more.

*See the Databases section for more details.

Output Files

A MetaPhlAn run will output 2 files into output_path:

  • out.txt: Results of the MetaPhlAn run.
  • {input_file_name}.bowtie2out.txt: The intermediate Bowtie 2 output file generated by MetaPhlAn. This can be passed in as input to quickly rerun with the same input. This is not generated if --no-mapis passed via tool_args

Tool Versions

Toolchest currently supports version 3.0.14 of MetaPhlAn.

Databases

Toolchest currently supports the latest version of the mpa_v30_CHOCOPhlAn_201901_marker_info database. You can read more about the database on the Github wiki.


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